Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules

AutoDock Vina is an open-source program for doing molecular docking

A molecular simulation program with broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques including QM/MM, MM/CG, and a range of implicit solvent models.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.